Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF CD1D-LIPID-ANTIGEN COMPLEXED WITH BETA-2-MICROGLOBULIN, NKT15 ALPHA-CHAIN AND NKT15 BETA-CHAIN
 
Authors :  N. A. Borg
Date :  25 Apr 07  (Deposition) - 03 Jul 07  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Cd1D-Lipid Antigen Nkt15 Complex, Lipid Binding Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. A. Borg, K. S. Wun, L. Kjer-Nielsen, M. C. Wilce, D. G. Pellicci, R. Koh, G. S. Besra, M. Bharadwaj, D. I. Godfrey, J. Mccluskey, J. Rossjohn
Cd1D-Lipid-Antigen Recognition By The Semi-Invariant Nkt T-Cell Receptor.
Nature V. 448 44 2007
PubMed-ID: 17581592  |  Reference-DOI: 10.1038/NATURE05907

(-) Compounds

Molecule 1 - T-CELL SURFACE GLYCOPROTEIN CD1D
    ChainsA, E
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System PlasmidPFASTBAC DUAL
    Expression System Taxid7111
    Expression System Vector TypePLASMID
    GeneCD1D
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCD1D ANTIGEN, R3G1
 
Molecule 2 - BETA-2-MICROGLOBULIN
    ChainsB, F
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System PlasmidPFASTBAC DUAL
    Expression System Taxid7111
    Expression System Vector TypePLASMID
    FragmentBETA-2-MICROGLOBULIN
    GeneB2M
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - NKT15 ALPHA-CHAIN
    ChainsC, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 4 - NKT15 BETA-CHAIN
    ChainsD, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)ABCD    
Biological Unit 2 (1x)    EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1AGH2Ligand/IonN-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
2BMA1Ligand/IonBETA-D-MANNOSE
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1AGH1Ligand/IonN-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
2BMA1Ligand/IonBETA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1AGH1Ligand/IonN-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
2BMA-1Ligand/IonBETA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:24 , ASN A:42 , NAG A:1100BINDING SITE FOR RESIDUE NAG A 1000
2AC2SOFTWARENAG A:1000 , BMA A:1200BINDING SITE FOR RESIDUE NAG A 1100
3AC3SOFTWARENAG A:1100BINDING SITE FOR RESIDUE BMA A 1200
4AC4SOFTWAREALA A:19 , ASN A:20 , TRP A:23BINDING SITE FOR RESIDUE NAG A 2000
5AC5SOFTWAREASN E:20 , SER E:22 , NAG E:3100BINDING SITE FOR RESIDUE NAG E 3000
6AC6SOFTWARETRP E:23 , NAG E:3000BINDING SITE FOR RESIDUE NAG E 3100
7AC7SOFTWARETHR E:24 , ASN E:42 , ASP E:43BINDING SITE FOR RESIDUE NAG E 4000
8AC8SOFTWARECYS A:12 , LEU A:29 , HIS A:38 , TRP A:40 , PHE A:70 , TYR A:73 , SER A:76 , PHE A:77 , ASP A:80 , LEU A:90 , ASP A:151 , TRP A:153 , THR A:154 , PRO C:28 , PHE C:29 , SER C:30 , ARG C:95 , GLY C:96BINDING SITE FOR RESIDUE AGH C 208
9AC9SOFTWARELEU E:13 , GLN E:14 , TRP E:40 , TYR E:73 , SER E:76 , PHE E:77 , ASP E:80 , PHE E:84 , LEU E:90 , PHE E:118 , ASP E:151 , TRP E:153 , THR E:154 , PHE E:169 , PHE G:29 , SER G:30 , ARG G:95 , GLY G:96BINDING SITE FOR RESIDUE AGH E 2

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:102 -A:166
2A:206 -A:261
3B:25 -B:80
4C:22 -C:90
5C:139 -C:189
6C:164 -D:174
7D:23 -D:92
8D:148 -D:213
9E:102 -E:166
10E:206 -E:261
11F:25 -F:80
12G:22 -G:90
13G:139 -G:189
14G:164 -H:174
15H:23 -H:92
16H:148 -H:213

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Trp A:277 -His A:278
2Lys B:6 -Ile B:7
3Val B:27 -Ser B:28
4His B:31 -Pro B:32
5Ser C:6 -Pro C:7
6Ser C:27 -Pro C:28
7Thr D:7 -Pro D:8
8Tyr D:154 -Pro D:155
9Leu E:7 -Phe E:8
10Thr E:154 -Arg E:155
11His F:31 -Pro F:32
12Ser G:6 -Pro G:7
13Ser G:27 -Pro G:28
14Thr H:7 -Pro H:8
15Lys H:31 -Met H:32
16Tyr H:154 -Pro H:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_010211T64SCD1D_HUMANPolymorphism62621276A/ET46S
2UniProtVAR_076691D96NB2MG_HUMANDisease (AMYL8)398122820B/FD76N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_010211T64SCD1D_HUMANPolymorphism62621276AT46S
2UniProtVAR_076691D96NB2MG_HUMANDisease (AMYL8)398122820BD76N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_010211T64SCD1D_HUMANPolymorphism62621276ET46S
2UniProtVAR_076691D96NB2MG_HUMANDisease (AMYL8)398122820FD76N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.B2MG_HUMAN98-104
 
  2B:78-84
F:78-84
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.B2MG_HUMAN98-104
 
  1B:78-84
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.B2MG_HUMAN98-104
 
  1-
F:78-84

(-) Exons   (4, 7)

Asymmetric Unit (4, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003681711ENSE00001208284chr1:158149737-158149952216CD1D_HUMAN-00--
1.2ENST000003681712ENSE00001446474chr1:158150609-158150952344CD1D_HUMAN1-21210--
1.3ENST000003681713ENSE00001039119chr1:158151245-158151511267CD1D_HUMAN21-110902A:6-92
E:6-92
87
87
1.4ENST000003681714ENSE00001039117chr1:158151822-158152100279CD1D_HUMAN110-203942A:92-185
E:92-185
94
94
1.5ENST000003681715ENSE00001690740chr1:158152668-158152946279CD1D_HUMAN203-296942A:185-278
E:185-277
94
93
1.6ENST000003681716ENSE00001308386chr1:158153726-158153825100CD1D_HUMAN296-329341A:278-280
-
3
-
1.7ENST000003681717ENSE00001446472chr1:158153919-158154686768CD1D_HUMAN329-33570--

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:275
 aligned with CD1D_HUMAN | P15813 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:275
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293     
           CD1D_HUMAN    24 RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWGGS 298
               SCOP domains d2po6a2 A:6-183 CD1, alpha-1 and alpha-2 domains                                                                                                                                  d2po6a1 A:184-277 CD1, alpha-3 domain                                                         --- SCOP domains
               CATH domains 2po6A01 A:6-182 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                      2po6A02 A:183-280 Immunoglobulins                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.........eeeeeee..eeeeee.......ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeee.....eeeeeeeee..eeeeeee..eeee.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......eeeeeeeeeee.....eeeee.........eeeeeee.....eeeeeeeeee.hhh...eeeee........eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:6-92 UniProt: 21-110 [INCOMPLETE]                                     --------------------------------------------------------------------------------------------Exon 1.5  PDB: A:185-278 UniProt: 203-296                                                     -- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------Exon 1.4  PDB: A:92-185 UniProt: 110-203                                                      --------------------------------------------------------------------------------------------1.6 Transcript 1 (2)
                 2po6 A   6 RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWHHH 280
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275     

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with B2MG_HUMAN | P61769 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:99
                                    30        40        50        60        70        80        90       100       110         
           B2MG_HUMAN    21 IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM 119
               SCOP domains d2po6b1 B:1-99 beta2-microglobulin                                                                  SCOP domains
               CATH domains 2po6B00 B:1-99 Immunoglobulins                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.........eeeeeeeeee....eeeeeee..ee....ee...ee.....eeeeeeeee.......eeeeeee......eeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------N----------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 2po6 B   1 IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM  99
                                    10        20        30        40        50        60        70        80        90         

Chain C from PDB  Type:PROTEIN  Length:203
 aligned with TCA_HUMAN | P01848 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:203
                                                                                                                                            1                                                                                          
                                     -         -         -         -         -         -         -         -         -         -         -  |      8        18        28        38        48        58        68        78        88   
            TCA_HUMAN     - ----------------------------------------------------------------------------------------------------------------PNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS  91
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2po6C01 C:1-116 Immunoglobulins                                                                                  ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee......eeeeeee......eeeeeee....eeee..eeee......eeeeee...hhhhh.eeeeeee........eee...eeeeee........eeeee........eeeeee...............eee.....eee....eee.eeeeee........................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2po6 C   1 NQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSNGRYTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS 206
                                    10        20        30        40        50        60|       71        81        91       103       113       123       133       143       153       163       173       183       193       203   
                                                                                      60|                                   100|                                                                                                       
                                                                                       62                                    103                                                                                                       

Chain D from PDB  Type:PROTEIN  Length:244
 aligned with TRBC1_HUMAN | P01850 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:244
                                                                                                                                              1                                                                                                                                 
                                     -         -         -         -         -         -         -         -         -         -         -    |    6        16        26        36        46        56        66        76        86        96       106       116       126    
          TRBC1_HUMAN     - ------------------------------------------------------------------------------------------------------------------EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 130
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2po6D01 D:2-118 Immunoglobulins                                                                                    2po6D02 D:119-244 Immunoglobulins                                                                                             --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeee......eeeeeeee..eeee.......ee.........eee...hhhhh.eeeeeee.........eee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2po6 D   2 ADIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGDLSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSGLRDRGLYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 247
                                    11        21        31        41        51        61 ||     72        82        92       102||     113       123       133       143       153       163       173       183       193       203       213       223       233       243    
                                                                                        63|                                   103|                                                                                                                                              
                                                                                         65                                    105                                                                                                                                              

Chain E from PDB  Type:PROTEIN  Length:272
 aligned with CD1D_HUMAN | P15813 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:272
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
           CD1D_HUMAN    24 RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYW 295
               SCOP domains d2po6e2 E:6-183 CD1, alpha-1 and alpha-2 domains                                                                                                                                  d2po6e1 E:184-277 CD1, alpha-3 domain                                                          SCOP domains
               CATH domains 2po6E01 E:6-182 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                      2po6E02 E:183-277 Immunoglobulins                                                               CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C1-set-2po6E01 E:194-274                                                         --- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C1-set-2po6E02 E:194-274                                                         --- Pfam domains (2)
         Sec.struct. author ....eeeeeeeeeee..eeeeeeeeee..eeeeee......eee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.....eeeeeeeee..eeeeeee..eeee......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......eeeeeeeeeee.....eee...........ee...ee.....eeeeeeeeee.hhh...eeeee........eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------S--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: E:6-92 UniProt: 21-110 [INCOMPLETE]                                     --------------------------------------------------------------------------------------------Exon 1.5  PDB: E:185-277 UniProt: 203-296 [INCOMPLETE]                                        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------Exon 1.4  PDB: E:92-185 UniProt: 110-203                                                      -------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2po6 E   6 RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYW 277
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275  

Chain F from PDB  Type:PROTEIN  Length:98
 aligned with B2MG_HUMAN | P61769 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:98
                                    31        41        51        61        71        81        91       101       111        
           B2MG_HUMAN    22 QRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM 119
               SCOP domains d2po6f1 F:2-99 beta2-microglobulin                                                                 SCOP domains
               CATH domains 2po6F00 F:2-99 Immunoglobulins                                                                     CATH domains
           Pfam domains (1) ---------C1-set-2po6F01 F:11-92                                                            ------- Pfam domains (1)
           Pfam domains (2) ---------C1-set-2po6F02 F:11-92                                                            ------- Pfam domains (2)
         Sec.struct. author ....eeeeee.........eeeeeeeeee.....eeeeee..ee.........ee.....eeeeeeeee.......eeeeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------N----------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 2po6 F   2 QRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM  99
                                    11        21        31        41        51        61        71        81        91        

Chain G from PDB  Type:PROTEIN  Length:204
 aligned with TCA_HUMAN | P01848 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:204
                                                                                                                                            1                                                                                           
                                     -         -         -         -         -         -         -         -         -         -         -  |      8        18        28        38        48        58        68        78        88    
            TCA_HUMAN     - ----------------------------------------------------------------------------------------------------------------PNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSP  92
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2po6G01 G:1-116 Immunoglobulins                                                                                  ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee......eeeeeee.....eeeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeeee........eee...eeeeee........eeeee........eeeeee...............eee.....eeehhhheee.eeeeee......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2po6 G   1 NQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSNGRYTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSP 207
                                    10        20        30        40        50        60|       71        81        91       103       113       123       133       143       153       163       173       183       193       203    
                                                                                      60|                                   100|                                                                                                        
                                                                                       62                                    103                                                                                                        

Chain H from PDB  Type:PROTEIN  Length:244
 aligned with TRBC1_HUMAN | P01850 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:244
                                                                                                                                              1                                                                                                                                 
                                     -         -         -         -         -         -         -         -         -         -         -    |    6        16        26        36        46        56        66        76        86        96       106       116       126    
          TRBC1_HUMAN     - ------------------------------------------------------------------------------------------------------------------EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 130
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2po6H01 H:2-118 Immunoglobulins                                                                                    2po6H02 H:119-244 Immunoglobulins                                                                                             --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeee.......eeeeeeee..eeee.......ee.........eee...hhhhh.eeeeeee.........eee...eeeeee.hhhhh...eeeee..hhhhhhhh.eeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2po6 H   2 ADIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGDLSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSGLRDRGLYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 247
                                    11        21        31        41        51        61 ||     72        82        92       102||     113       123       133       143       153       163       173       183       193       203       213       223       233       243    
                                                                                        63|                                   103|                                                                                                                                              
                                                                                         65                                    105                                                                                                                                              

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 6)

Asymmetric Unit

(-) CATH Domains  (2, 12)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)
2a2po6B00B:1-99
2b2po6C01C:1-116
2c2po6G01G:1-116
2d2po6D01D:2-118
2e2po6H01H:2-118
2f2po6D02D:119-244
2g2po6H02H:119-244
2h2po6A02A:183-280
2i2po6E02E:183-277
2j2po6F00F:2-99

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Ig (577)
(-)
Family: C1-set (338)
1aC1-set-2po6F01F:11-92
1bC1-set-2po6F02F:11-92
1cC1-set-2po6E01E:194-274
1dC1-set-2po6E02E:194-274

(-) Gene Ontology  (81, 99)

Asymmetric Unit(hide GO term definitions)
Chain A,E   (CD1D_HUMAN | P15813)
molecular function
    GO:0030881    beta-2-microglobulin binding    Interacting selectively and non-covalently with beta-2-microglobulin.
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0030883    endogenous lipid antigen binding    Interacting selectively and non-covalently with an endogenous cellular lipid antigen.
    GO:0030884    exogenous lipid antigen binding    Interacting selectively and non-covalently with an exogenous lipid antigen (examples include microbial lipids and glycolipids).
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0030882    lipid antigen binding    Interacting selectively and non-covalently with a lipid antigen.
    GO:0071723    lipopeptide binding    Interacting selectively and non-covalently with a lipopeptide, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds and containing a nonprotein group consisting of a lipid or lipids.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0045058    T cell selection    The process in which T cells that express T cell receptors that are restricted by self MHC protein complexes and tolerant to self antigens are selected for further maturation.
    GO:0048006    antigen processing and presentation, endogenous lipid antigen via MHC class Ib    The process in which an antigen-presenting cell expresses lipid antigen of endogenous origin in association with an MHC class Ib protein complex on its cell surface. Class Ib here refers to non-classical class I molecules, such as those of the CD1 family.
    GO:0048007    antigen processing and presentation, exogenous lipid antigen via MHC class Ib    The process in which an antigen-presenting cell expresses lipid antigen of exogenous origin in association with an MHC class Ib protein complex on its cell surface. Class Ib here refers to non-classical class I molecules, such as those of the CD1 family.
    GO:0016045    detection of bacterium    The series of events in which a stimulus from a bacterium is received and converted into a molecular signal.
    GO:0034113    heterotypic cell-cell adhesion    The attachment of a cell to a cell of a different type via adhesion molecules.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0045089    positive regulation of innate immune response    Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B,F   (B2MG_HUMAN | P61769)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0033077    T cell differentiation in thymus    The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus.
    GO:0019731    antibacterial humoral response    An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
    GO:0019885    antigen processing and presentation of endogenous peptide antigen via MHC class I    The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class I protein complex. The peptide antigen is typically, but not always, processed from a whole protein. Class I here refers to classical class I molecules.
    GO:0002479    antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
    GO:0002480    antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a pathway not requiring TAP (transporter associated with antigen processing). The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell. Class I here refers to classical class I molecules.
    GO:0002481    antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class Ib protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family.
    GO:0002474    antigen processing and presentation of peptide antigen via MHC class I    The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0071281    cellular response to iron ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    GO:0010977    negative regulation of neuron projection development    Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:1900121    negative regulation of receptor binding    Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
    GO:0002726    positive regulation of T cell cytokine production    Any process that activates or increases the frequency, rate, or extent of T cell cytokine production.
    GO:0001916    positive regulation of T cell mediated cytotoxicity    Any process that activates or increases the frequency, rate or extent of T cell mediated cytotoxicity.
    GO:1904434    positive regulation of ferrous iron binding    Any process that activates or increases the frequency, rate or extent of ferrous iron binding.
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:1900122    positive regulation of receptor binding    Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
    GO:0048260    positive regulation of receptor-mediated endocytosis    Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:1904437    positive regulation of transferrin receptor binding    Any process that activates or increases the frequency, rate or extent of transferrin receptor binding.
    GO:0042026    protein refolding    The process carried out by a cell that restores the biological activity of an unfolded or misfolded protein, using helper proteins such as chaperones.
    GO:0050690    regulation of defense response to virus by virus    Any viral process that modulates the frequency, rate, or extent of the antiviral response of the host cell or organism.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0003254    regulation of membrane depolarization    Any process that modulates the rate, frequency or extent of membrane depolarization. Membrane depolarization is the process in which membrane potential changes in the depolarizing direction from the resting potential, usually from negative to positive.
    GO:0046686    response to cadmium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0002237    response to molecule of bacterial origin    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
    GO:0001895    retina homeostasis    A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
cellular component
    GO:0012507    ER to Golgi transport vesicle membrane    The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:1990712    HFE-transferrin receptor complex    A protein complex containing at least HFE and a transferrin receptor (either TFR1/TFRC or TFR2), proposed to play a role in the sensing of transferrin-bound Fe (Fe2-Tf) on the plasma membrane to regulate hepcidin transcription.
    GO:0042612    MHC class I protein complex    A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031905    early endosome lumen    The volume enclosed by the membrane of an early endosome.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C,G   (TCA_HUMAN | P01848)
biological process
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain D,H   (TRBC1_HUMAN | P01850)
biological process
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    AGH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His B:31 - Pro B:32   [ RasMol ]  
    His F:31 - Pro F:32   [ RasMol ]  
    Leu E:7 - Phe E:8   [ RasMol ]  
    Lys B:6 - Ile B:7   [ RasMol ]  
    Lys H:31 - Met H:32   [ RasMol ]  
    Ser C:27 - Pro C:28   [ RasMol ]  
    Ser C:6 - Pro C:7   [ RasMol ]  
    Ser G:27 - Pro G:28   [ RasMol ]  
    Ser G:6 - Pro G:7   [ RasMol ]  
    Thr D:7 - Pro D:8   [ RasMol ]  
    Thr E:154 - Arg E:155   [ RasMol ]  
    Thr H:7 - Pro H:8   [ RasMol ]  
    Trp A:277 - His A:278   [ RasMol ]  
    Tyr D:154 - Pro D:155   [ RasMol ]  
    Tyr H:154 - Pro H:155   [ RasMol ]  
    Val B:27 - Ser B:28   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2po6
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  B2MG_HUMAN | P61769
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  CD1D_HUMAN | P15813
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TCA_HUMAN | P01848
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TRBC1_HUMAN | P01850
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  105200
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  B2MG_HUMAN | P61769
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CD1D_HUMAN | P15813
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TCA_HUMAN | P01848
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TRBC1_HUMAN | P01850
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        B2MG_HUMAN | P617691a1m 1a1n 1a1o 1a6z 1a9b 1a9e 1agb 1agc 1agd 1age 1agf 1akj 1ao7 1b0g 1b0r 1bd2 1c16 1ce6 1cg9 1de4 1duy 1duz 1e27 1e28 1eey 1eez 1efx 1exu 1gzp 1gzq 1hhg 1hhh 1hhi 1hhj 1hhk 1hla 1hsa 1hsb 1i1f 1i1y 1i4f 1i7r 1i7t 1i7u 1im3 1im9 1jf1 1jgd 1jge 1jht 1jnj 1k5n 1kpr 1ktl 1lds 1lp9 1m05 1m6o 1mhe 1mi5 1n2r 1of2 1oga 1ogt 1onq 1p7q 1py4 1q94 1qew 1qlf 1qqd 1qr1 1qrn 1qse 1qsf 1qvo 1r3h 1s8d 1s9w 1s9x 1s9y 1sys 1syv 1t1w 1t1x 1t1y 1t1z 1t20 1t21 1t22 1tmc 1tvb 1tvh 1uqs 1ur7 1uxs 1uxw 1vgk 1w0v 1w0w 1w72 1x7q 1xh3 1xr8 1xr9 1xz0 1ydp 1ypz 1zhk 1zhl 1zs8 1zsd 1zt4 1zvs 2a83 2ak4 2av1 2av7 2axf 2axg 2bck 2bnq 2bnr 2bsr 2bss 2bst 2bvo 2bvp 2bvq 2c7u 2cii 2cik 2clr 2d31 2d4d 2d4f 2dyp 2e8d 2esv 2f53 2f54 2f74 2f8o 2fyy 2fz3 2git 2gj6 2gt9 2gtw 2gtz 2guo 2h26 2h6p 2hjk 2hjl 2hla 2hn7 2j8u 2jcc 2nw3 2nx5 2p5e 2p5w 2pye 2rfx 2uwe 2v2w 2v2x 2vb5 2vlj 2vlk 2vll 2vlr 2x4n 2x4o 2x4p 2x4q 2x4r 2x4s 2x4t 2x4u 2x70 2x89 2xks 2xku 2xpg 2ypk 2ypl 2yxf 2z9t 3am8 3b3i 3b6s 3bgm 3bh8 3bh9 3bhb 3bo8 3bp4 3bp7 3bvn 3bw9 3bwa 3bxn 3bze 3bzf 3c9n 3cdg 3cii 3ciq 3czf 3d18 3d25 3d2u 3d39 3d3v 3dbx 3dhj 3dhm 3dtx 3dx6 3dx7 3dx8 3dxa 3ekc 3ffc 3fqn 3fqr 3fqt 3fqu 3fqw 3fqx 3ft2 3ft3 3ft4 3giv 3gjf 3gsn 3gso 3gsq 3gsr 3gsu 3gsv 3gsw 3gsx 3h7b 3h9h 3h9s 3hae 3hcv 3hg1 3hla 3hpj 3huj 3i6g 3i6k 3i6l 3ib4 3ixa 3jts 3kla 3kpl 3kpm 3kpn 3kpo 3kpp 3kpq 3kpr 3kps 3kww 3kxf 3kyn 3kyo 3l3d 3l3g 3l3i 3l3j 3l3k 3lkn 3lko 3lkp 3lkq 3lkr 3lks 3ln4 3ln5 3low 3loz 3lv3 3m17 3m1b 3mgo 3mgt 3mr9 3mrb 3mrc 3mrd 3mre 3mrf 3mrg 3mrh 3mri 3mrj 3mrk 3mrl 3mrm 3mrn 3mro 3mrp 3mrq 3mrr 3mv7 3mv8 3mv9 3myj 3myz 3mzt 3na4 3nfn 3o3a 3o3b 3o3d 3o3e 3o4l 3ov6 3ox8 3oxr 3oxs 3pwj 3pwl 3pwn 3pwp 3qda 3qdg 3qdj 3qdm 3qeq 3qfd 3qfj 3qzw 3rew 3rl1 3rl2 3rwj 3s6c 3sdx 3sjv 3skm 3sko 3spv 3t8x 3tid 3tie 3tlr 3tm6 3to2 3tzv 3u0p 3upr 3utq 3uts 3utt 3v5d 3v5h 3v5k 3vcl 3vfm 3vfn 3vfo 3vfp 3vfr 3vfs 3vft 3vfu 3vfv 3vfw 3vh8 3vri 3vrj 3vwj 3vwk 3vxm 3vxn 3vxo 3vxp 3vxr 3vxs 3vxu 3w0w 3w39 3wl9 3wlb 3wuw 3x11 3x12 3x13 3x14 4e0k 4e0l 4e5x 4en3 4eup 4f7m 4f7p 4f7t 4ftv 4fxl 4g8g 4g8i 4g9d 4g9f 4gkn 4gks 4gup 4hkj 4hwz 4hx1 4i48 4i4w 4jfd 4jfe 4jff 4jfo 4jfp 4jfq 4jqv 4jqx 4jrx 4jry 4k71 4k7f 4kdt 4l29 4l3c 4l3e 4l4t 4l4v 4lcw 4lcy 4lhu 4lnr 4m8v 4mj5 4mj6 4mji 4mnq 4n0f 4n0u 4n8v 4nnx 4nny 4no0 4no2 4no3 4no5 4nqc 4nqd 4nqe 4nqv 4nqx 4nt6 4o2c 4o2e 4o2f 4ono 4pj5 4pj7 4pj8 4pj9 4pja 4pjb 4pjc 4pjd 4pje 4pjf 4pjg 4pjh 4pji 4pjx 4pr5 4pra 4prb 4prd 4pre 4prh 4pri 4prn 4prp 4qok 4qrp 4qrq 4qrr 4qrs 4qrt 4qru 4r9h 4ra3 4rah 4rmq 4rmr 4rms 4rmt 4rmu 4rmv 4rmw 4u1h 4u1i 4u1j 4u1k 4u1l 4u1m 4u1n 4u1s 4u6x 4u6y 4uq2 4uq3 4wc8 4wdi 4wj5 4wo4 4wu5 4wu7 4wuu 4ww2 4wwk 4x0s 4x6c 4x6d 4x6e 4x6f 4xxc 4z76 4z77 4z78 4zez 5b38 5b39 5bjt 5brz 5bs0 5bxf 5c07 5c08 5c09 5c0a 5c0b 5c0c 5c0d 5c0e 5c0f 5c0g 5c0i 5c0j 5c9j 5cfh 5cka 5ckg 5cs7 5csb 5csg 5d2l 5d2n 5d5m 5d7i 5d7j 5d7l 5d9s 5ddh 5def 5deg 5e00 5e6i 5e9d 5enw 5eo0 5eo1 5eot 5eu3 5eu4 5eu5 5eu6 5euo 5f7d 5f9j 5fa3 5fa4 5fdw 5gr7 5gsb 5gsr 5gsv 5gsx 5hga 5hgb 5hgd 5hgh 5hhm 5hhn 5hho 5hhp 5hhq 5hyj 5ib1 5ib2 5ib3 5ib4 5ib5 5ieh 5iek 5im7 5inc 5ind 5iro 5isz 5iue 5j1a 5jhd 5jzi 5knm 5l2j 5l2k 5men 5meo 5mep 5meq 5mer 5n1y 5swq 5t6w 5t6x 5t6y 5t6z 5t70 5u16 5u17 5u1r 5u2v 5u6q 5u72 5v5l 5v5m 5vgd 5vge 5xos 5xot 5xov
        CD1D_HUMAN | P158131zt4 3huj 3sdx 3tzv 3u0p 3vwj 3vwk 4en3 4lhu 4mng 4mq7 4wo4 4ww2 4wwk
        TCA_HUMAN | P018481ao7 1bd2 1fyt 1j8h 1kgc 1mi5 1oga 1qrn 1qsf 1ymm 1zgl 2ak4 2bnq 2bnr 2bnu 2cdf 2cdg 2esv 2eyr 2eys 2eyt 2f53 2f54 2gj6 2ial 2iam 2ian 2nx5 2p5e 2p5w 2pye 2pyf 2vlj 2vlk 2vlm 2vlr 2xn9 2xna 3arb 3ard 3are 3arf 3arg 3d39 3dx9 3dxa 3ffc 3gsn 3he7 3hg1 3kpr 3kps 3kxf 3o4l 3o6f 3o8x 3o9w 3pwp 3qdg 3qdj 3qdm 3qeq 3qeu 3qib 3qjf 3qux 3scm 3sda 3sdc 3sdd 3sdx 3sjv 3skn 3t0e 3tn0 3tvm 4apq 4c56 4g8e 4g8f 4irs 4jfd 4jfe 4jff 4jfh 4jrx 4jry 4mvb 4mxq 4n0c 4n5e 4nhu 4onh 4p4k 4prh 4pri 4prp 4udt 4udu 4ww1 4ww2 4wwk 4x6b 4x6c 4x6d 4y16 4y2d 4y4f 4y4h 4y4k 4zdh 4zez 5brz 5bs0 5c07 5c08 5c09 5c0a 5c0b 5c0c 5eu6 5fk9 5fka 5hhm 5hho 5hyj 5ks9 5ksa 5ksb
        TRBC1_HUMAN | P018501ao7 1fyt 1j8h 1kgc 1ktk 1mi5 1oga 1ymm 1zgl 2ak4 2axh 2bnq 2bnr 2bnu 2cde 2cdf 2cdg 2esv 2f53 2f54 2gj6 2ial 2iam 2ian 2nts 2nw2 2nx5 2p5e 2p5w 2pye 2pyf 2vlj 2vlk 2vlm 2vlr 2xn9 2xna 3arb 3ard 3are 3arf 3arg 3d39 3d3v 3dx9 3dxa 3ffc 3he6 3hg1 3kpr 3kps 3o4l 3tn0 4g8e 4g8f 4gg6 4gg8 4iiq 4jfd 4jfe 4jff 4jfh 4jrx 4jry 4l4t 4l4v 4l9l 4lcc 4lcw 4mji 4mnq 4nqc 4nqd 4nqe 4ozf 4ozg 4ozh 4ozi 4p46 4prh 4pri 4prp 4x6b 4x6c 4x6d 4zdh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2PO6)